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Home , Pseudoextinction

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Answers are given below for calculations, problems, and short 4. It is an accident in the sense that other codes with the same answers; a reference to the relevant section(s) of the chapter is four letters could work equally well. It is frozen in the sense given for longer answers and definitions or explanations of that changes in it are selected against. See Section 3.8. technical terms; or a reference to further reading is given for 5. This is intended more as a discussion topic: for the idea see topics not explicitly discussed in the text. Section 3.9. 6. Because a form would have existed in time before the series Chapter 1 of fossils (of vertebrates from fish to mammals) that can be 1. See Section 1.1. strongly argued to be its ancestors. 2. . 3. The popular concept had as progressive, with Chapter 4 ascending a one-dimensional line from lower 1. forms to higher. Evolution in Darwin’s theory is tree-like Number (as Proportion of Proportion of and branching, and no species is any “higher” than any density/m2) original cohort original cohort other a forms are adapted only to the environments they Age interval surviving to surviving to dying during live in. (days) day x day x interval 4. Darwin’s theory of and Mendel’s theory of heredity. 0–250 100 100 0.9989 251–500 0.11 0.11 0.273 Chapter 2 501–750 0.08 0.08 0.75 1. The terms are explained in the chapter. 751–1,000 0.06 0.06 – 2. (i) 100% AA; (ii) 1 AA :1 Aa; (iii) 1 AA :2 Aa :1 aa; (iv) 100% AB/AB; and (v) 100% AB/AB. 2. (a) See Section 4.2. (b) In technical terms, drift (on which 3. As fractions: (i) 1/4 AB, 1/4 Ab, 1/4 aB, 1/4 ab; and see Chapter 6). The gene frequencies would change between (ii) (1– r)/2 AB, (1 − r)/2 ab, r/2 Ab, r/2 aB. As ratios: (i) 1 AB : generations because there is heritability (condition 2) and 1 Ab :1 aB :1 ab; and (ii) (1 − r) AB : (1 − r) ab : r Ab : r aB. some individuals produce more offspring than others (condition 3). But if the differences in reproduction are not Chapter 3 systematically associated with some character or other, the 1. Approximately the species level; the pigeon example might changes in gene frequency between generations will be ran- stretch it to genera, but higher categories do not evolve in dom or directionless. (c) No evolution at all. If the character human lifetimes. conferring higher than average fitness is not inherited by the 2. (i) If you look at any one time and place, living things usually individual’s offspring, natural selection cannot increase its fall into distinct, recognizable groups that could be called frequency in the population. “kinds.” (ii) If you look over a range of space (if the “kinds” 3. The requirements of inheritance and association between high in question are species) the kinds break down; if you look reproductive success and some character have also to be met. through a range of times (if the kinds are species or any 4. The mechanism has to: (i) perceive the change in environ- higher category) the kinds also break down. The differences ment; (ii) work out what the appropriate adaptation is to between higher categories can also be broken down by study- the new environment; (iii) alter the genes in the germ line ing the full range of diversity on Earth: you might think that in a manner to code for the new adaptation. (i) is possible; plants and animals are less clear categories after studying the (ii) could vary from possible in a case such as simple range of unicellular organisms. camouflage to impossible in a case requiring a new complex 3. (a), (b), and (d) are homologies; (c) is an analogy. adaptation, such as the for living on land of the

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first terrestrial tetrapods; and (iii) would contradict what is we do need the second- assumption that these factors known about genetics and it is difficult to see how it could be are the same for all genotypes.) done. The mechanism would have to work backwards from 6. AA 1/2; aa 1/2. The gene frequencies are 0.5 and the Hardy– the new phenotype (something like a long neck in a giraffe) Weinberg ratio 1/4 : 1/2 : 1/4. The observed to expected to deduce the needed genetic changes, even though the phe- ratios are 2/3 : 4/3 : 2/3, which when scaled to a maximum notype was produced by multiple, interacting genetic and of 1 give the fitnesses 1/2:1:1/2. environmental effects. 7. (a) 0.5; and (b) 0.5625. You need equation 5.13; t = 1. For 5. (a) Directional selection (for smaller brains); (b) stabilizing (a) it looks like this: 0.625 = 0.5 + (0.75 − 0.5)(1 − m). And selection; and (c) no selection. for (b) it looks like this: x = 0.5 + (0.625 − 0.5)(1 − 0.5). 6. (a) Here are two arguments. (i) If every pair produced two 8. (a) The aa genotype is likely to be fixed. If aa mate only offspring, natural selection would favor new genetic variants among themselves and AA and Aa mate only with AA and that produced three, or more, offspring. After the more Aa, whenever there is an Aa × Aa mating, some aa progeny fecund form had spread through the population the average are produced, who will subsequently only mate with other would still be two but the greater competition among indi- aa individuals. (b) Now AA mate only with AA, Aa with Aa, viduals to survive would lead to variation in the success of and aa with aa. The homozygous matings preserve their the broods of different parents. (ii) Random accidents alone genotypes, but when Aa mate together they produce 1/4 aa will guarantee that some individuals fail to breed; then for and 1/4 AA progeny. In an extreme case, the population the average to be two, as it must be for any population that diverges into two species, one AA the other aa and the is reasonably stable in the long term, all successfully repro- heterozygotes are lost. (c) (i) The dominant allele will be ducing individuals will produce more than two offspring. fixed; and (ii) the recessive allele will be fixed. (b) Ecologists discuss this in terms of r and K selection, or life history theory: in some environments there is little competi- ps(1 − ) 9. p′ = tion and selection favors producing large numbers of small 12 −− p2 s pqs offspring; whereas in others there is massive competition and selection favors producing fewer offspring and investing The denominator can be variously rearranged. a large amount in each. Many other factors can also operate. m 10. p* ≈ Chapter 5 s 1. Populations 1 and 5 are in Hardy–Weinberg equilibrium; populations 2–4 are not. As to why they are not, in popula- The derivation starts with the equilibrium condition, tion 4 it looks like AA is lethal, in 2 there may be a hetero- p2s = qm. We then note that q ≈ 1, and p2s ≈ m; divide both zygote advantage, and in 3 a heterozygote disadvantage. sides by s and take square roots. Population 2 could also be produced by disassortative mating, and 3 by assortative mating. In population 3 there Chapter 6 could also be a Wahlund effect. All the deviations are 1. Either 100% A or 100% a (there is an equal chance of each). so large that random sampling is unlikely to be the whole 2. See (a) Section 6.1, and (b) Section 6.3. explanation. 3. (1) 0.5; (2) 0.5; (3) 0.375; and (4) 0. See Section 6.5. 2. (a) p2/(1 − sq2); (b) p/(1 − sq2); and (c) 1 − sq2. 4. (a) and (b) 10−8. Population size cancels out in the formula 3. (1/3)(3 − s) = 1 − (s/3). for the rate of neutral evolution. 4. If you do it in your head, s ≈ 0.1. To be exact, 5. (a) 1/(2N); and (b) (1 − (1/(2N)). s = 0.095181429619. 6. Both manipulations requires substituting 1 − H for f and 5. That the fitness differences are in survivorship (not fertil- then some canceling and multiplying though by −1 to make ity), and in particular in survivorship during the life stage the sign positive. investigated in the mark–recapture experiment. (By the way, mark–recapture experiments are also used by eco- Chapter 7 logists to estimate absolute survival rates: they require the 1. See Figure 7.1a and b. additional assumptions that the animals do not become 2. The main observations suggesting neutral molecular evolu- “trap shy” or “trap happy,” and that the mark and release tion are not also seen in morphology. This was discussed for treatment does not reduce survival. These assumptions are the constancy of evolutionary rates in Section 7.3. The other not needed when estimating relative survival. However, original observations (for absolute rates and heterozygosities,

.. 692 Answers to Study and Review Questions

and for the relation between rate and constraint) either have 2. Populations 1 and 4 may show fitness epistasis, in which, in

not been made, or such observations as there are do not sug- population 1, A1 has higher fitness in combination with B1 gest that the problems found in selective explanations for than with B2, and vice versa in poulation 2. Fitnesses are also apply to morphology. independent (maybe multiplicative or additive) in popula- 3. (i) A high rate of evolution; (ii) high levels of ; tions 2 and 3. (iii) a constant rate of evolution; and (iv) functionally more 3. Populations 1 and 2 should equilibrate at haplotype fre- constrained changes have lower evolutionary rates. quencies of 1/4, 1/4, 1/4, and 1/4 for the four haplotypes; 4. (i) The molecular clock is not constant enough; (ii) genera- populations 3 and 4 should equilibrate at 1/9, 2/9, 2/9, and tion time effects seem to differ between synonymous and 4/9. Populations 2 and 3 are already at equilibrium and non-synonymous substitutions; (iii) is too should not change through time; populations 1 and 4 will similar between species with different population sizes, and evolve toward the equilibrium frequencies at a rate deter- heterozygosity is too low in species with high N; and (iv) [not mined by the recombination rate between the two loci. discussed in the text, but for completeness] rates of evolu- 4. Observed heterozygosities are arguably a little on the low tion do not have a predicted relation with levels of genetic side for the neutral theory (Section 7.6); the effect of a sec- variation. tion at one locus is on average to reduce heterozygosities at 5. (a) The key variable in the neutral explanation is the chance linked loci, producing a net reduction in average hetero- that a is neutral: it is arguably higher for regions zygosity through the genome. with less functional constraints (Section 7.6.2). (b) The key 5. See Figure 8.8b. The equilibrium is at the top of the hill. variable in the selective explanation is the chance that a mutation has a small rather than large effect, and so may Chapter 9 cause a fine-tuning improvement (Section 7.6.2). 1. See Section 9.2, particularly Figures 9.3 and 9.4. In statist- 6. No; the main evidence is from codon usage biases (Section ical theory, the argument is formalized as the central limit 7.11.4). theorem. 7. (a) This is a fairly standard figure. Non-synonymous sub- 2. +1. The answer is incomplete without the sign. = = = = 2 = = stitutions are rarer, probably because more of them are 3. (a) VP 300/8 37.5; VA 48/8 6; and h 6/37.5 6.16. deleterious than synonymous substitutions. It could be that (b) +3: you add the additive effects inherited from each almost all evolution for both kinds of change is by neutral parent. drift. (b) Either selection has positively favored amino acid 4. 106. changes, elevating the rate of non-synonymous evolution, 5. This is not explicitly discussed in the chapter, but see Sec- or selection has been relaxed and non-synonymous changes tion 13.x (p. 000). You might predict it will evolve toward a that are normally disadvantageous are here neutral. (c) It canalizing type relation, as in Figure 9.11b, because then an looks like selection is driving amino acid changes in the pro- individual is most likely to have the optimal phenotype. tein coded for by this gene. 6. It will go through an intermediate phase with many recombinant genotypes produced by crossing-over between Chapter 8 the three initial ; it should end up with only 1. the chromosomal type that yields the optimal character by Frequency of means of a homozygote: all +++−−−−−.

A B A B D Population 1 1 1 1 Value of Chapter 10 1. They cannot explain adaptation. There is no reason except + 1 7/16 1/2 1/2 3/16 chance why a new genetic variant should be in the direction 2 1/4 1/2 1/2 0 of improved adaptation, and random chance change will not 3 1/9 1/3 1/3 0 produce adaptation. If (as in the “Lamarckian” theory) the − 4 11/162 1/3 1/3 7/162 new genetic variants are in the direction of adaptation, it implies there is some adaptive mechanism behind the pro- Note that the haplotype frequency is found by the sum duction of new variants. Natural selection is the only known of homozygotes plus 1/2 the heterozygotes (as for a gene theory that could explain such a mechanism.

frequency, Section 5.1). If you have figures in the A1B1 2. See Figures 10.2 and 10.3. frequency column for population 1 such as 11/16 or 14/16 3. Superficially, yes, but the adaptive information a all the

you may have not divided the frequency of A1B1/A1B2 by 2. metabolic processes of the cyanobacteria that evolved

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photosynthesis a probably evolved in small steps and therefore for an individual to produce more copies of a gene may be nothing deep in Fisher’s or Darwin’s arguments is violated. improved more by helping relatives than by breeding more 4. (a) Many small steps; and (b) some larger initial steps, fol- itself. Group selection requires more awkward conditions lowed by more small steps a the full distribution may be a (see question 2!). negative exponential (Orr 1998). 5. The average individual is likely to be worse off, as Figure 5. No, it just turned out that way. Sometimes, by chance, an B11.1 illustrates. Competition between individuals reduces that works well in one function turns out to work well the efficiency of the group. Whole bodies would have the in another function after relatively little adjustment. same problem if there were no mechanisms to suppress 6. (a) (i) Natural selection, in the form of negative selection. competition between genes, or cells, within a body. The absent regions represent maladaptive forms which, 6. (a) The whole genome; and (b) the . when they arise as , are selected out. (ii) Develop- mental constraint. Something about the way the organisms Chapter 12 develop embryonically makes it impossible, or at least dif- 1. (a) 33%; and (b) 67%. ficult, for these forms to arise. (b) Four kinds of evidence 2. (a) Crudely, it has to be high; more exactly, a total deleteri- were mentioned in Section 10.7.3. The kind that most was ous mutation rate of more than one per organism per gener- said about was the use of artificial selection: if the character ation is needed. On its realism, see the end of Section 12.2.2: can be altered, its form is unlikely to be due to constraint. the evidence is inconclusive and neither rules it out or in. (b) Relation 1 in Figure 12.6. The y-axis is logarithmic. Chapter 11 Relation 2 corresponds to independent fitness effects, in 1. Many answers are possible, but the main examples in this which sex (before the 50% cost) is indifferent. Relation 3 is chapter were: (a) adaptations for finding food; (b) eating as the diminishing returns type of epistasis, in which sex is much food as possible to maximize reproductive rate; or positively daft, even before the 50% cost. Again, you can cannibalism; or destructive fighting; or producing a 50 : 50 argue reality either way: see the end of Section 12.2.2. sex ratio in a polygynous species; (c) restraining reproduc- 3. The material in the text (Section 12.2.3) would suggest look- tion to preserve the local food supply; and (d) segregation ing at the relation between the frequency of sex and para- distortion in which the total fertility of the organism is sitism in taxa that can reproduce both ways; or looking into reduced. the genetics of host–parasite relations and measuring the 2. You might explain it in terms of two factors, the relative frequency of resistance genes in hosts or penetration genes rates of of altruistic and selfish groups and the rate in parasites. Other answers would be possible too, going of migration. Or you might reduce them to the one vari- beyond the textual materials. able m, which is the average number of successful emigrants 4. See Section 12.4.4: if the character were cheap to produce, produced by a selfish group during the time the group males of all genetic qualities would evolve to produce it. exists (before it goes extinct). The fate of the model is then 5. See Section 12.4.3: a female who did not choose extreme determined by whether m is greater or smaller than 1 males would on average mate with a less extreme male than (Section 11.2.5). would other females in the population; she would produce 3. b can be estimated as the number of extra offspring pro- less extreme than average sons; and they would grow up into duced by the nests with helpers: 2.2 − 1.24 ≈ 1. But that a population in which most females prefer extreme males. is produced by 1.7 helpers, giving b ≈ 1/1.7 ≈ 0.6. c can be Her sons would have low reproductive success and their estimated either as zero (if the helper has no other option) or mother’s lack of preference would be selected against. as the number of offspring produced by an unhelped pair 6. See Section 12.5.1: if more daughters than sons were pro- (if it could breed alone), in which case c = 1.24. With r = 1/2 duced by most members of the population, the fitness of a it should help if it cannot breed alone but should breed if male would be higher than that of a female. Individuals who it can. This way of estimating b and c does have problems, produced more sons than daughters would be favored by however. selection. A sex ratio of one is a stable point at which there is 4. Kin selection applies to a family group, or more generally no advantage to producing more offspring of either sex. a group of kin (indeed it is not theoretically necessary that 7. (a) Positive, and (b) negative frequency-dependent selection. the kin live in groups, though they do have to be able to 8. (a) Yes, and (b) no. When different levels of selection con- influence one another’s fitness); group selection, at least in flict, adaptation cannot be perfect at all levels. You can find the pure sense, applies to groups of unrelated individuals. another example of a constraint on perfection in Holland & Kin selection is a plausible process, because the conditions Rice’s (1999) imposed monogamy experiment.

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Chapter 13 4. The intermediate stages (heterozygotes) would be selected 1. Look at Section 13.2. against.

2. (i) 1, (ii) 2, and (iii) 1. 5. (a) “When in the F1 offspring of the two different animal 3. See Section 13.3, particularly Table 13.1. races one sex is absent, rare, or sterile, that sex is the

4. GST is 0 for species 1, 0.5 for species 2, and 0 for species 3. heterozygous one” (Section 14.4.6). (b) Males. (c) By Biological factors influencing GST include: the recency of postulating that some of the genes in the Dobzhansky– origin of the species, the speed of evolution, how uniform Muller theory are on the X chromosome, and recessive the environment is through space, and the amount of gene (Box 14.1). flow between populations. 6. Valley crossing means that evolution passes through 5. It can be argued both ways; see the second part of Section a phase in which fitness goes down. (a) No, (b) no, and 13.7.2. If asexual species are discrete in the same way that (c) yes. sexual species seem to be, that suggests the force maintain- 7. Reproductive character displacement, or character dis- ing species as discrete clusters is ecological rather than placement for prezygotic isolation. There are two main interbreeding. explanations. (i) Reinforcement. Females in allopatry have 6. (i) Typological; (ii) population (or so I would argue); not been selected to discriminate against heterospecific (iii) population; (iv) two schools of thought implicitly argue males, because in evolutionary history the ancestors of the it each way (do you think we have a set number of real, modern females have never met those males; females in distinct emotions?); (v) typological; and (vi) most would sympatry are descended from females that have been argue typological, I suspect, but Hull (1988) makes the exposed to both kinds of male. Females who mated with opposite case, that scientific theories are like biological heterospecific males produced hybrid offspring of low species. fitness, so selection favored discrimination. (ii) Without 7. See the work of Grant and Grant described in Section 13.7.3. reinforcement. There are various versions of the alternative Chapter 14 contains more material on the genetic theory of explanation; the one most explained in the text (Section postzygotic isolation. 16.8) is as follows. Different individuals of the two species 8. (i) (a), (b), and (c) (probably) yes; (ii) (a) yes, (b) and (c) no; in the past may have shown various degrees of isolation and (iii) (a), (b), and (c) can be yes. from the other species. In areas where they now coexist in sympatry, if reproductive isolation was low, the two species Chapter 14 would fuse and probably now look more like one of the 1. Pleiotropy and hitch-hiking (Section 14.3.2), perhaps species (and so be classified as a member of it); if reproduct- partly due to (Section 14.11). Figure 14.3 ive isolation was high, the two would coexist and remain shows an example from Darwin’s finches. distinct. Thus only where isolation was high do we now see 2. (a) Postzygotic isolation can be expressed by the fitness the two species in sympatry. In areas where the species are reduction of hybrid offspring compared with offspring now allopatric, whatever the reproductive isolation, they of crosses within a population (or within a near species). continue to exist. Thus the average isolation will be lower (b) The index we saw (Figure 14.2) was (number of matings than for sympatry. to same type − number of matings to other type)/(total 8. Theoretical reasons: the conditions required for reinforce- number of matings), which gives: (i) I = 1; (ii) I = 0.5; and ment maybe too short lived. Empirical reasons: the evid- (iii) I = 0. ence from artificial selection is poor, and the evidence from 3. It shows that the neighboring populations are more closely reproductive character displacment is open to alternative related: the northeast populations are more closely related interpretations. to the southeast populations than to any other populations 9. (a) “Secondary”: in separate popula- (such as southwest or northwest). It could have been that tions occurred in the past, followed by range expansion, the populations evolved from formerly fragmented ranges, and the two populations come into contact at what is now a and expanded to the current distribution, but the phy- hybrid zone. (b) “Primary”: a stepped cline evolved within logeny suggests a gradual evolution of the current songs in the population, which became large enough for the forms the current places. Also, the phylogeny shows that the gap on either side of the step to be recognized as distinct taxo- in the range on the east side is probably only because there nomic forms. is a desert; there is an underlying continuity. The still 10. See Figure 14.14. On sympatric , the closest relat- evolved in a ring, with the northeast birds derived from the ives of a species should live in the same area; on allopatric southeast birds. speciation, the closest relatives should be in a different area.

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Chapter 15 7. When more than one evolutionary change underlies an 1. observed difference (or identity) between two sequences. 8. (a) (1 − 3p)3p2; (b) 16. × × ABCDE ABCDE BACDE 9. 2 3 1. Chapter 16 1. See Table 16.1.

Evolutionary: paraphyletic, monophyletic. Cladistic: monophyletic. CABDE DECBA DECBA Phenetic: polyphyletic, paraphyletic, monophyletic.

2. (i) Cow (lungfish, salmon); (ii) cow (lungfish, salmon); (iii) (cow, lungfish), salmon. See the end of Section 16.3. 3. (i) The Euclidean distances are obtained by Pythagoras’s theorem, and I picked the numbers to give a 3, 4, 5 triangle: EDCBA the three species can be drawn on a graph with one character per axis. (ii) The mean character distance is the average of the distances for the two characters. See Section 16.5.

Species 1 Species 2 Species 3

Species 1 3 4

Species 2 1.5 5 2. Species 3 2 3.5

A D The two distance measures imply contradictory groupings of the three species. This is a case where the classification chosen by the numeric phenetic method would be ambigu- ous, and therefore arguably subjective. E 4. (a) 2.31; (b) 2.5; (c) species 1 and 2 equally; (d) with a nearest nearest neighbor cluster statistic the grouping is (1,2)(3(4,5)); with a nearest average neighbor cluster statistic it is ((1,2)3) B C (4,5); and (e) see Section 16.5 for the moral. 5. A critic would reply that the same problem would resurface in another form. Maybe the average and nearest neighbor statistics in the case of Figure 14.5 could be made to agree by adding five further characters. However, those two are just 3. Evolutionary rates are approximately equal in all lineages. two of many cluster statistics, and the result would almost 4. See Section 15.4. certainly still be ambiguous with respect to some other clus- 5. A is ancestral and A′ derived in all three, but the inference is ter statistic. The ambiguity could only be removed if there most certain in (a) and least certain in (c). (If A is ancestral in were one non-ambiguous phenetic hierarchy in nature, and the group of species 1 + 2, then the minimum number of there is no reason to suppose such a hierarchy exists. events in (a), (b), and (c), respectively, are 2, 3, and 3; 6. (a) The difference reflects evolutionary theory’s scientific whereas if A′ were ancestral, the minimums would be 3, 4, peculiarity as a historic theory. The hierarchy in a phyloge- and 4.) netic classification is historic, and is used for the reasons dis- 6. See Section 15.8. cussed in the chapter. The periodic table is non-historic and

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non-hierarchical. Its structure represents two of the funda- Chapter 18 mental properties that determine the nature of an element, 1. See Section 18.1 and Figure 18.1. and the position of an element in the table can be used to 2. Using the rounded figure of 1.2 × 10−4 for the decay constant: predict what the element will be like. The position of an organism in a phylogenetic classification cannot be used to 14 14 predict much about what the organism will be like. Much C : N Age more could be said about the nature of different theories in (a) 1 : 1 5,776 science, and the way different theories imply different kinds of classifications. (b) See Section 16.8! (b) 2 : 1 3,379

Chapter 17 (c) 1 : 2 9,155 1. See Section 17.1 and Figure 17.2. 2. Going down the column: 1/2, 1/2, 1/2, and 1. 3. My first three counts gave 26, 27, and 26 dispersal events 3. RNA can be single-stranded, allowing both and from older to younger islands, and 13, 12, and 12 dispersals replication in one molecule. RNA can also have many from younger to older islands, respectively! The correct shapes, enabling many reactions, including catalysis. answer is something close to these numbers, but you have 4. There are several possibilities. (i) The molecular evidence is the idea if your figures are in this region. Compare Figure wrong, for instance because of an error in calibration or non- 17.6. There is no reason why there should be so many more constant rates of evolution. (ii) The fossil date is wrong, for dispersal events from older to younger islands if speciation instance because the record is incomplete or a fossil has been was created by splitting a larger range, whereas it makes sense misdated. (iii) The estimates concern different events a the if it was the result of dispersal because the older island would molecular clock gives a time of common ancestor, and the have been occupied first. fossil evidence gives a time of proliferation. 4. 5. See Section 18.5. 6. The mammals evolved in many stages, and the changes were Area K K K O M O M M M H H M M M M M in adaptive characters. Species 1 2 3 4 6 5 7 9 10 11 12 8 13 15 16 14 7. (i) Brain size, (ii) bipedality, and (iii) jaw reduction and associated changes in teeth. You might also mention changes in cultural, social, and linguistic behavior, and even changes in the thumb and big toe in the hand and foot.

Chapter 19 1. (a) By the molecular clock. (b) Several answers are possible, but the chapter noticed, for instance, the 2R hypothesis about the origin of vertebrates, and the possible association of gene duplications with the origin of dicotyledons. 2. (i) Gene transfer between bacteria and humans, or (ii) gene loss in a lineage leading to worms and fruitflies. They can be tested once we have an expanded knowledge of the Some minor variants would also be possible, depending on phylogenetic distribution of the genes (see Figure 19.3). how ancestral species like species 8 and 14 are represented. 3. Genes on the X and Y chromosomes do not recombine, 5. (a)–(b), (a)–(c), and (e)–(f) are congruent. (a)–(d), (a)–(f), and will have been diverging since recombination stopped. (c)–(d), (c)–(f), (e)–(b), and (e)–(d) are incongruent. The four regions of gene similarity suggest that recombina- 6. There are two main hypotheses. (i) The competitive sup- tion was shut down in four stages, perhaps by inversions. eriority of North American mammals, perhaps due to a Autosomal genes recombine and this prevents them from history of more intense competition, and reflected in their diverging. relative encephalization. (ii) Environmental change, such that the North American mammals were competitively Chapter 20 superior in South American environments after the 1. (a) Pedomorphosis; and (b) neoteny and progenesis (see Interchange. Table 20.1).

.. Answers to Study and Review Questions 697

2. The eyes of insects and vertebrates are at some level homo- Chapter 22 logous, but not necessarily as eyes. The gene, for instance, 1. (a) and host shifts are more likely when could simply be a regional selector for a certain part of the hosts are phylogenetically closer. (b) Host shifts that are head, that happens to have eyes in these two taxa. Altern- independent of phylogeny, for instance between hosts that atively, the common ancestor may have had eyes of some are chemically similar but phylogenetically distant. sort, developmentally controlled by the gene, but the struc- 2. Biologists have seen whether the diversity of each tures we now observe as eyes in insects and vertebrates still increases simultaneously in the fossil record. They have built up independently in evolution. also made phylogenetically controlled comparisons between 3. (a) Evolvability is the chance that a species will undergo plants that do and do not interact with insects to see if the evolutionary change. The “evolutionary change” in the defini- former have higher diversity. (And phylogenetically con- tion could refer to: (i) any genetic change, (ii) change in the trolled comparisons between insects that do and do not form of speciation, or (iii) macroevolutionary, innovative interact with flowering plants to see if the former have higher change. (b) See Section 20.8: genetic switches enable genes diversity.) to be recruited to act in new circumstances. Genes can 3. Cophylogeny, and some evidence about the timing of the acquire new functions without compromising their old branches, for instance from molecular clocks. function. 4. In order of increasing virulence: (iv) < (i) < (ii) < (iii). (ii) and (iii) might be about the same, but this was not Chapter 21 specifically discussed in the text. See Ewald (1993). 1. 5. (a) See Section 22.6.1. Antagonistic biological interactions, x t x t 1 1 2 2 Rate such as between predator and prey, have evolved to become more dangerous over time: predators have become more 2 11 4 1 0.0693 dangerously armed, prey more powerfully defended. (b) The level of defensive adaptation in prey can be measured in 2 11 20 1 0.2303 such features as the thickness of molluskan shells and the habitats they occupy. Predatory adaptations have primarily 20 11 40 1 0.0693 been studied by the numbers of specialist as opposed to gen- eralist predators: the presence of specialists suggests a more 20 6 40 1 0.1386 dangerous condition. It is important to test escalation by the proportion of species types through time, because there is more of everything in more recent fossil records. See If you have answers like 0.2, 1.8, 2, and 4 you forgot to take Figures 22.12–22.14.

logs. If you have minus numbers you have x1 and x2, or t1 and 6. Antagonistic in general, and antagonistic co- t2, the wrong way round. evolution with a dynamic equilibrium in particular. Van 2. (a) An inverse relation (see Figure 21.3). (b) One possibility Valen suggested that total ecological resources may be con- is that long periods with rapid change and short periods with stant through time, and the selective pressure on a species is slow change have been excluded from the study, perhaps proportional to the loss of resources it suffers due to lagging because the former would transform the character beyond behind competing species. commensurability and the latter seemed unworthy of notice. 3. See Section 21.5. Chapter 23 4. There are three possible answers. (i) , 1. Because there was a lack of knowledge of the global dis- in which case is orthodox. (ii) Spe- tribution of species and (for large-bodied animals, whose ciation by valley crossing, in which case the theory is backing geographic distributions were best known) the difficulty an unorthodox a some would say discredited a theory of of assigning disarticulated fossil bone fragments to species speciation. (iii) Saltational macromutations, in which case (Section 23.1). the theory is unorthodox to the point of probably being 2. (a) In a real extinction all the members of a lineage die with- erroneous. out leaving descendants; in a pseudoextinction the lineage 5. The text contains two types of evidence: (i) rates of change in continues to reproduce but its taxonomic name changes in arbitrarily coded characters (see Figure 21.9), and (ii) taxo- mid-lineage, or the lineage persists but is temporarily un- nomic rates, in which the longevity of genera is represented in the fossil record (Lazarus taxa). See Box 23.1. longer than average (see Table 21.2). (b) Pseudoextinction of type (a) in Figure B23.1 snarls up

.. 698 Answers to Study and Review Questions

tests of both. If the of species with differ- developing species are more likely to be preserved) or by ing developmental modes in Figure 23.9, or in the test of their being more likely to survive local difficulties by their synchroneity in Figure 23.3, were pseudoextinctions, the dispersing larval stage. explanation for the trend, or synchronous pattern, would 7. Two possibilities we looked at are differences in speciation be something to do not with nature but with the habits or extinction rates caused by differences in adaptations of of taxonomists. Lazarus-type pseudoextinction would also different species, or by differential persistency of niches (see suggest the results are artifacts. Pseudoextinction of type Section 23.6.2). (b) in Figure B23.1 may be less damaging. (Also, the test 8. The heritability criterion is as relevant as ever here. In of the Red Queen hypothesis by survivorship curves in classic group selection problems, the character (such as Chapter 22 may be little damaged by either of the taxo- altruism) is disadvantageous to individuals but advant- nomic causes of pseudoextinction. The hypothesis might ageous to groups. Selfish individuals can invade groups. be recast in terms of rate of change rather than chance of Once the group is infected by selfishness, it loses altruism. extinction.) The character (altruism) is not inherited by groups for 3. (a) The iridium anomaly (Figure 23.4), perhaps combined long. In classic cases of species selection, there is no ques- with the dated Chicxulub crater. (b) The extinctions should tion of a species being invaded by some alternative adapta- be sudden and synchronous in all taxa, rather than gradual, tion. Selection favors different adaptations in different and they should not in general be preceded by reductions in species a direct development in some, planktonic develop- population size. For the difficulties of testing these predic- ment in others, for example. Those attributes are passed tions, look at Section 23.3.2. down from ancestral species to descendant species. Species 4. At the end of the Cretaceous and Permian (for the top two selection is possible because there is no conflict between extinctions); plus either the end Ordovician or the end individual and species selection; heritability therefore is Triassic (for the top three); plus the Devonian (for the top possible. Species selection is not a theory of the evolution of five). adaptation a only of the consequences of adaptations. 5. See Figure B23.2. The observed extinction rate in the earlier 9. See Figure 23.11. A double wedge pattern suggests a com- interval will be (a) high, and (b) low. petitive replacement. If one taxon goes extinct before the 6. At mass extinctions there is no relation. In background other radiates, it suggests non-competitive replacement. extinctions the taxa with planktonic development have an 10. Partly by different data compilations (with different taxo- extinction rate that is half that of taxa with direct develop- nomic make ups) but mainly by different statistical correc- ment. The background extinction difference can be ex- tions for biases in: (i) the amount of rock preserved from plained either by bias in the fossil record (if planktonically different times, and (ii) the amount of rock studied.

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